When checking collisions against an object with the mouse it is consistently incorrect. I'm not really sure how else to put it. The attached project shows the issue. Very clearly something is not right here.

Steps To Reproduce

1. Load GM and sample
2. Notice when you move the mouse left to right that the object that is highlighted is not correct
3. Notice you can click on the object though even though the mouse enter/leave is incorrect

The bounding boxes for these two sprites are wrong in this project, I suspect a bad version of the IDE saved them that way.
The Asset Compiler takes them and saves them out, the runner reads them in and uses them.

You can fix the sprites by opening them in the Sprite editor, and, say, drawing one pixel in the lower right corner, then deleting it and re-saving the sprites.